[ Started: 2025-02-22 00:25:35 CET ]
[ OmnipathR v3.15.9 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (0a92537 2025-02-13 19:46:14) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-02-12 r87715)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.9’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param) 
See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-02-22 00:26:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:02] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:26:02] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:26:02] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:26:02] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:26:02] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:26:02] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:26:03] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:26:03] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:26:03] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:03] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
ungroup:
  function(x, ...)
ungroup.tbl_attrs:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:12] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:26:12] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:26:12] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:26:12] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:26:12] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:26:12] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:26:12] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:26:12] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:26:12] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:12] [TRACE]   [OmnipathR] Cache locked: FALSE
ambiguity_summarize: no visible binding for global variable ‘data’
download_base : fun: no visible binding for global variable
  ‘resp_status_desc’
download_base : fun: no visible global function definition for
  ‘headers’
download_base : fun: no visible binding for global variable ‘response’
log_welcome: no visible binding for global variable ‘pkgname’
translate_ids : <anonymous>: no visible binding for global variable
  ‘From’
xls_downloader: possible error in download_to_cache(url_key = url_key,
  url_key_param = url_key_param, url_param = url_param, ext = ext,
  http_param = http_param, post = post): unused argument (http_param =
  http_param)
Undefined global functions or variables:
  From data headers pkgname resp_status_desc response
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'ambiguity.Rd'
  ‘from_col’ ‘to_col’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'::' or ':::' import not declared from: ‘httr’
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: all_uniprots
> ### Title: A table with all UniProt records
> ### Aliases: all_uniprots
> 
> ### ** Examples
> 
> human_swissprot_entries <- all_uniprots(fields = 'id')
[2025-02-22 00:26:36] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:36] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:36] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-22 00:26:36] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:26:36] [TRACE]   [OmnipathR] Downloaded 30.7 Kb in 0.397677s from www.ensembl.org (77.3 Kb/s); Redirect: 0s, DNS look up: 0.019897s, Connection: 0.038765s, Pretransfer: 0.098659s, First byte at: 0.381292s
[2025-02-22 00:26:37] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:37] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:26:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:26:37] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:26:37] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:26:37] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
Warning: Failed to open 'https://omabrowser.org/All/oma-species.txt': SSL connection timeout
[2025-02-22 00:26:47] [WARN]    [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: cannot open the connection
[2025-02-22 00:26:52] [TRACE]   [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:26:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:26:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
Warning: Failed to open 'https://omabrowser.org/All/oma-species.txt': SSL connection timeout
[2025-02-22 00:27:02] [WARN]    [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 2/3); error: cannot open the connection
[2025-02-22 00:27:07] [TRACE]   [OmnipathR] Attempt 3/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:27:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:27:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
Warning: Failed to open 'https://omabrowser.org/All/oma-species.txt': Failed to connect to omabrowser.org port 443 after 10003 ms: Timeout was reached
[2025-02-22 00:27:17] [ERROR]   [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 3/3); error: cannot open the connection
[2025-02-22 00:27:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:27:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:27:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:27:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:27:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:27:17] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:27:17] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:27:17] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `open.connection()`:
! cannot open the connection
Backtrace:
     ▆
  1. ├─OmnipathR::all_uniprots(fields = "id")
  2. │ └─organism %<>% ncbi_taxid
  3. ├─OmnipathR::ncbi_taxid(.)
  4. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
  5. ├─purrr::map_int(., taxon_name, "ncbi")
  6. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
  7. │   ├─purrr:::with_indexed_errors(...)
  8. │   │ └─base::withCallingHandlers(...)
  9. │   ├─purrr:::call_with_cleanup(...)
 10. │   └─OmnipathR (local) .f(.x[[i]], ...)
 11. │     ├─... %>% if_null_len0(NA)
 12. │     └─OmnipathR::get_db("organisms")
 13. │       └─OmnipathR::load_db(key, param = param)
 14. │         ├─rlang::exec(loader, !!!param)
 15. │         └─OmnipathR (local) `<fn>`()
 16. │           └─... %>% ...
 17. ├─OmnipathR:::if_null_len0(., NA)
 18. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 19. ├─OmnipathR:::is_empty_2(.)
 20. │ └─value %>% ...
 21. ├─dplyr::first(.)
 22. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 23. │   └─vctrs::vec_size(x)
 24. ├─dplyr::pull(., name_type)
 25. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 26. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 27. ├─dplyr::mutate(...)
 28. ├─dplyr::full_join(...)
 29. ├─dplyr:::full_join.data.frame(...)
 30. │ └─dplyr::auto_copy(x, y, copy = copy)
 31. │   ├─dplyr::same_src(x, y)
 32. │   └─dplyr:::same_src.data.frame(x, y)
 33. │     └─base::is.data.frame(y)
 34. ├─oma_organisms() %>% select(-genome_source, -oma_version)
 35. ├─dplyr::select(., -genome_source, -oma_version)
 36. ├─OmnipathR::oma_organisms()
 37. │ └─... %>% ...
 38. ├─dplyr::mutate(...)
 39. ├─OmnipathR:::generic_downloader(...)
 40. │ ├─... %>% omnipath_cache_save(url = url, post = post)
 41. │ ├─rlang::exec(...)
 42. │ └─OmnipathR (local) `<fn>`(...)
 43. │   └─base::stop(result)
 44. ├─OmnipathR::omnipath_cache_save(., url = url, post = post)
 45. │ └─base::saveRDS(data, target_path)
 46. └─purrr (local) `<fn>`(`<smplErrr>`)
 47.   └─cli::cli_abort(...)
 48.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Caused by error in `map_int()`:
  ℹ In index: 1.
  Caused by error in `open.connection()`:
  ! cannot open the connection
  Class:   purrr_error_indexed/rlang_error/error/condition
  ── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ─────────
  Error in `eval(code, test_env)`: object 'response' not found
  Backtrace:
      ▆
   1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13
   2. └─tidyr::separate_rows(., sources, sep = ";")
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-02-22 00:28:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:04] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:28:04] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:28:04] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:28:04] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:28:04] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:28:04] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:28:05] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:28:05] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:28:05] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Contains 2 files.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-02-22 00:28:05] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:05] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:05] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-22 00:28:05] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Downloaded 30.9 Kb in 0.462429s from www.ensembl.org (66.8 Kb/s); Redirect: 0s, DNS look up: 0.001376s, Connection: 0.019958s, Pretransfer: 0.092301s, First byte at: 0.445295s
[2025-02-22 00:28:05] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:05] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-22 00:28:05] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.109458s from omabrowser.org (987 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.011513s, Pretransfer: 0.044291s, First byte at: 0.05851s
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:28:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:06] [TRACE]   [OmnipathR] Downloaded 2.2 Mb in 0.34009s from omnipathdb.org (6.4 Mb/s); Redirect: 0s, DNS look up: 0.000975s, Connection: 0.017018s, Pretransfer: 0.05858s, First byte at: 0.090747s
[2025-02-22 00:28:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:28:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:07] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-02-22 00:28:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-02-22 00:28:07] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-02-22 00:28:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:07] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:11] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:14] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Downloaded 906.3 Kb in 0.223959s from omnipathdb.org (4 Mb/s); Redirect: 0s, DNS look up: 0.001075s, Connection: 0.022658s, Pretransfer: 0.055754s, First byte at: 0.099779s
[2025-02-22 00:28:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:14] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-02-22 00:28:14] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:14] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:15] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:16] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.298123s from omnipathdb.org (7.1 Mb/s); Redirect: 0s, DNS look up: 0.000936s, Connection: 0.022495s, Pretransfer: 0.056919s, First byte at: 0.100593s
[2025-02-22 00:28:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:17] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:28:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:28:17] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-02-22 00:28:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:17] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:19] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-02-22 00:28:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-02-22 00:28:19] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-02-22 00:28:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Downloaded 1.4 Mb in 0.237552s from omnipathdb.org (6.1 Mb/s); Redirect: 0s, DNS look up: 0.000937s, Connection: 0.020544s, Pretransfer: 0.054258s, First byte at: 0.093868s
[2025-02-22 00:28:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:20] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-02-22 00:28:20] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:20] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:20] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:20] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Downloaded 1 Mb in 0.212283s from omnipathdb.org (4.9 Mb/s); Redirect: 0s, DNS look up: 0.000948s, Connection: 0.018558s, Pretransfer: 0.067147s, First byte at: 0.103039s
[2025-02-22 00:28:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:21] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-22 00:28:21] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:21] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:21] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-22 00:28:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-22 00:28:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-22 00:28:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Downloaded 60 bytes in 0.07974s from omnipathdb.org (752 bytes/s); Redirect: 0s, DNS look up: 0.001126s, Connection: 0.0185s, Pretransfer: 0.061915s, First byte at: 0.079686s
[2025-02-22 00:28:22] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:22] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-02-22 00:28:22] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:22] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:22] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-02-22 00:28:22] [FATAL]   [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-22 00:28:23] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:28:23] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-22 00:28:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-22 00:28:23] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-22 00:28:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Downloaded 22.3 Kb in 0.119745s from omnipathdb.org (185.9 Kb/s); Redirect: 0s, DNS look up: 0.000869s, Connection: 0.021672s, Pretransfer: 0.074987s, First byte at: 0.116553s
[2025-02-22 00:28:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:23] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-02-22 00:28:23] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:23] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:23] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:28:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:24] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Downloaded 36.9 Kb in 0.105183s from omnipathdb.org (350.7 Kb/s); Redirect: 0s, DNS look up: 9e-04s, Connection: 0.020687s, Pretransfer: 0.056099s, First byte at: 0.096704s
[2025-02-22 00:28:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:24] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-22 00:28:24] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:24] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:24] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:24] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:28:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:27] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-22 00:28:27] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:28:27] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-02-22 00:28:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-02-22 00:28:27] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-02-22 00:28:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:28] [TRACE]   [OmnipathR] Downloaded 6.1 Mb in 0.696146s from omnipathdb.org (8.7 Mb/s); Redirect: 0s, DNS look up: 0.000998s, Connection: 0.018475s, Pretransfer: 0.067965s, First byte at: 0.102818s
[2025-02-22 00:28:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-02-22 00:28:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:28] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-02-22 00:28:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-02-22 00:28:30] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-02-22 00:28:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:30] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:30] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.071152s from omnipathdb.org (122.5 Kb/s); Redirect: 0s, DNS look up: 0.001104s, Connection: 0.018783s, Pretransfer: 0.051931s, First byte at: 0.070986s
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:31] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-02-22 00:28:31] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:49] [TRACE]   [OmnipathR] Downloaded 126.2 Kb in 17.879119s from rest.uniprot.org (7.1 Kb/s); Redirect: 0s, DNS look up: 0.01012s, Connection: 0.028832s, Pretransfer: 0.086451s, First byte at: 0.601794s
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-02-22 00:28:50] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:50] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:50] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-02-22 00:28:50] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:52] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:28:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:28:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:28:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:28:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:28:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:28:52] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:28:52] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:28:52] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Contains 14 files.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-02-22 00:28:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Downloaded 30.8 Kb in 0.395029s from www.ensembl.org (77.9 Kb/s); Redirect: 0s, DNS look up: 0.001867s, Connection: 0.020343s, Pretransfer: 0.091216s, First byte at: 0.377824s
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:28:53] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:53] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.106952s from omabrowser.org (1010.2 Kb/s); Redirect: 0s, DNS look up: 0.001042s, Connection: 0.010765s, Pretransfer: 0.043141s, First byte at: 0.055956s
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:28:54] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:54] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:54] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-22 00:28:54] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.331085s from omnipathdb.org (6.4 Mb/s); Redirect: 0s, DNS look up: 0.001102s, Connection: 0.021021s, Pretransfer: 0.053817s, First byte at: 0.093542s
[2025-02-22 00:28:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:54] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:28:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:28:55] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-02-22 00:28:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:55] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-02-22 00:28:57] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-02-22 00:28:57] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:28:57] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-02-22 00:28:57] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:28:57] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:33:57] [WARN]    [OmnipathR] Failed to download `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` (attempt 1/3); error: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]: Operation timed out after 300001 milliseconds with 0 bytes received
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] Attempt 2/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] Downloaded 1015 bytes in 0.056568s from www.ensembl.org (17.5 Kb/s); Redirect: 0s, DNS look up: 0.009935s, Connection: 0.028918s, Pretransfer: 0.028989s, First byte at: 0.056419s
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-02-22 00:34:02] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:02] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-02-22 00:34:02] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <html>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <head>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <style>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] html,
[2025-02-22 00:34:02] [WARN]    [OmnipathR] body {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] padding: 0;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] margin: 0;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] height: 100%;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] body {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] display: grid;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] font-size: 90%;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] h1 {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] h2 {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] h3 {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] header {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] grid-row: header;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] padding: 5px;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] height: 60px;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] background-color: #333366;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] header img {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] width: 185px;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] height: 45px
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] main {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] grid-row: main;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] padding: 20px;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] .mirrors {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] margin-top: 20px;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] padding: 10px;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] footer {
[2025-02-22 00:34:02] [WARN]    [OmnipathR] grid-row: footer;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] padding: 0 20px;
[2025-02-22 00:34:02] [WARN]    [OmnipathR] }
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </style>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </head>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <body>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <header>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </header>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <main>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <p>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-02-22 00:34:02] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-02-22 00:34:02] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </p>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <div class="mirrors">
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <ul>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </ul>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-02-22 00:34:02] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-02-22 00:34:02] [WARN]    [OmnipathR] data centre.
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </div>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </main>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <footer>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] <p>&copy; 2024 EMBL-EBI</p>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </footer>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </body>
[2025-02-22 00:34:02] [WARN]    [OmnipathR] </html>
[2025-02-22 00:34:02] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records

Quitting from lines 176-179 [omnipath] (cosmos.Rmd)
Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
The size of `nm` (2) must be compatible with the size of `x` (1).
--- failed re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:34:04] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:34:04] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Contains 5 files.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-22 00:34:04] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Downloaded 30.8 Kb in 0.34028s from www.ensembl.org (90.5 Kb/s); Redirect: 0s, DNS look up: 0.00134s, Connection: 0.020164s, Pretransfer: 0.101471s, First byte at: 0.324267s
[2025-02-22 00:34:05] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:05] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:34:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:05] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:34:05] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.123127s from omabrowser.org (877.5 Kb/s); Redirect: 0s, DNS look up: 0.001033s, Connection: 0.012699s, Pretransfer: 0.054744s, First byte at: 0.069397s
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:34:05] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:05] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-22 00:34:06] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-02-22 00:34:06] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:06] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-02-22 00:34:06] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:24] [TRACE]   [OmnipathR] Downloaded 126.2 Kb in 18.172221s from rest.uniprot.org (6.9 Kb/s); Redirect: 0s, DNS look up: 0.000933s, Connection: 0.019612s, Pretransfer: 0.088167s, First byte at: 0.784399s
[2025-02-22 00:34:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-02-22 00:34:24] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-02-22 00:34:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:24] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-02-22 00:34:24] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-02-22 00:34:24] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:34:37] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:34:37] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Contains 4 files.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-22 00:34:37] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:37] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Downloaded 30.9 Kb in 0.416023s from www.ensembl.org (74.2 Kb/s); Redirect: 0s, DNS look up: 0.001388s, Connection: 0.019744s, Pretransfer: 0.077109s, First byte at: 0.396087s
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.107741s from omabrowser.org (1002.8 Kb/s); Redirect: 0s, DNS look up: 0.000908s, Connection: 0.011433s, Pretransfer: 0.043615s, First byte at: 0.056813s
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:34:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.287134s from omnipathdb.org (7.4 Mb/s); Redirect: 0s, DNS look up: 0.009141s, Connection: 0.029836s, Pretransfer: 0.062076s, First byte at: 0.103844s
[2025-02-22 00:34:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:39] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:34:39] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:39] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-02-22 00:34:41] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:34:45] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:34:45] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Contains 4 files.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-22 00:34:45] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:34:45] [TRACE]   [OmnipathR] Downloaded 30.8 Kb in 0.380708s from www.ensembl.org (80.9 Kb/s); Redirect: 0s, DNS look up: 0.00138s, Connection: 0.019958s, Pretransfer: 0.07634s, First byte at: 0.362702s
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.109083s from omabrowser.org (990.4 Kb/s); Redirect: 0s, DNS look up: 0.00103s, Connection: 0.01156s, Pretransfer: 0.044128s, First byte at: 0.057723s
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-02-22 00:34:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:34:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:34:47] [TRACE]   [OmnipathR] Downloaded 3.5 Mb in 0.457229s from omnipathdb.org (7.6 Mb/s); Redirect: 0s, DNS look up: 0.063278s, Connection: 0.082002s, Pretransfer: 0.141452s, First byte at: 0.179144s
[2025-02-22 00:34:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-02-22 00:34:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:47] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:34:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-02-22 00:34:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-02-22 00:34:48] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-02-22 00:34:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:34:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:34:48] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-02-22 00:34:48] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-02-22 00:34:56] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-22 00:40:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-22 00:40:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-22 00:40:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] Downloaded 1.9 Mb in 0.267154s from omnipathdb.org (6.9 Mb/s); Redirect: 0s, DNS look up: 0.000969s, Connection: 0.018908s, Pretransfer: 0.052792s, First byte at: 0.088683s
[2025-02-22 00:40:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:23] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-02-22 00:40:23] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:23] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:23] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-22 00:40:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-22 00:40:24] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-22 00:40:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Downloaded 5.1 Kb in 0.081945s from omnipathdb.org (62.2 Kb/s); Redirect: 0s, DNS look up: 0.001001s, Connection: 0.016859s, Pretransfer: 0.065821s, First byte at: 0.081926s
[2025-02-22 00:40:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:24] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-02-22 00:40:24] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:24] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:24] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-02-22 00:40:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:27] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:40:27] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:40:27] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:40:27] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:40:27] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:40:27] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:40:27] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:40:28] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:40:28] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Contains 6 files.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-02-22 00:40:28] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:28] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:28] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-22 00:40:28] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:28] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Downloaded 31 Kb in 0.416652s from www.ensembl.org (74.3 Kb/s); Redirect: 0s, DNS look up: 0.010232s, Connection: 0.028734s, Pretransfer: 0.084727s, First byte at: 0.395955s
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.11226s from omabrowser.org (962.4 Kb/s); Redirect: 0s, DNS look up: 0.000952s, Connection: 0.011537s, Pretransfer: 0.045036s, First byte at: 0.058199s
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:29] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] Downloaded 1.6 Mb in 0.237739s from omnipathdb.org (6.7 Mb/s); Redirect: 0s, DNS look up: 0.000965s, Connection: 0.019708s, Pretransfer: 0.052676s, First byte at: 0.088989s
[2025-02-22 00:40:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:30] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-02-22 00:40:30] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:30] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:32] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:36] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] Downloaded 1.2 Mb in 0.232048s from omnipathdb.org (5.2 Mb/s); Redirect: 0s, DNS look up: 0.000937s, Connection: 0.021114s, Pretransfer: 0.053627s, First byte at: 0.093984s
[2025-02-22 00:40:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:37] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-02-22 00:40:37] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:37] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:38] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Organism(s): 10116
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Downloaded 438.4 Kb in 0.156289s from omnipathdb.org (2.7 Mb/s); Redirect: 0s, DNS look up: 0.001002s, Connection: 0.018181s, Pretransfer: 0.051843s, First byte at: 0.086928s
[2025-02-22 00:40:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:39] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-02-22 00:40:39] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:39] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:39] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:39] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Downloaded 188.5 Kb in 0.131655s from omnipathdb.org (1.4 Mb/s); Redirect: 0s, DNS look up: 0.000937s, Connection: 0.018903s, Pretransfer: 0.052018s, First byte at: 0.088933s
[2025-02-22 00:40:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:40] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-02-22 00:40:40] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:40] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:40] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:40] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.2834s from omnipathdb.org (7.5 Mb/s); Redirect: 0s, DNS look up: 0.000944s, Connection: 0.020286s, Pretransfer: 0.053703s, First byte at: 0.092918s
[2025-02-22 00:40:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:41] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:40:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:40:41] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-02-22 00:40:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:41] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:43] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:40:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:40:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:40:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:44] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Downloaded 264.9 Kb in 0.131047s from omnipathdb.org (2 Mb/s); Redirect: 0s, DNS look up: 0.000942s, Connection: 0.016138s, Pretransfer: 0.049666s, First byte at: 0.081577s
[2025-02-22 00:40:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:45] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-02-22 00:40:45] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:45] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:45] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:45] [TRACE]   [OmnipathR] Downloaded 25.1 Kb in 0.084966s from omnipathdb.org (294.9 Kb/s); Redirect: 0s, DNS look up: 0.001146s, Connection: 0.017043s, Pretransfer: 0.050305s, First byte at: 0.082315s
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:46] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Downloaded 2.2 Kb in 0.090562s from omnipathdb.org (23.8 Kb/s); Redirect: 0s, DNS look up: 0.000992s, Connection: 0.020397s, Pretransfer: 0.07111s, First byte at: 0.090546s
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:46] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] Downloaded 906.3 Kb in 0.225976s from omnipathdb.org (3.9 Mb/s); Redirect: 0s, DNS look up: 0.000926s, Connection: 0.020228s, Pretransfer: 0.069698s, First byte at: 0.108316s
[2025-02-22 00:40:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:47] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-02-22 00:40:47] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:47] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:48] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-02-22 00:40:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-02-22 00:40:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-02-22 00:40:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:49] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-22 00:40:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:51] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:52] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Downloaded 446.1 Kb in 0.191226s from omnipathdb.org (2.3 Mb/s); Redirect: 0s, DNS look up: 9e-04s, Connection: 0.020882s, Pretransfer: 0.070009s, First byte at: 0.110489s
[2025-02-22 00:40:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:52] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-02-22 00:40:52] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:52] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:53] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-22 00:40:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-22 00:40:53] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-22 00:40:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:53] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] Downloaded 270.4 Kb in 0.155063s from omnipathdb.org (1.7 Mb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.018432s, Pretransfer: 0.06766s, First byte at: 0.102638s
[2025-02-22 00:40:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:54] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-02-22 00:40:54] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:54] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:54] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations]
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-02-22 00:40:55] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-02-22 00:40:55] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-02-22 00:40:55] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Downloaded 15 Kb in 0.084767s from omnipathdb.org (176.6 Kb/s); Redirect: 0s, DNS look up: 0.000965s, Connection: 0.017675s, Pretransfer: 0.051148s, First byte at: 0.084433s
[2025-02-22 00:40:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:55] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-02-22 00:40:55] [INFO]    [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1]
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:55] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:55] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records.
[2025-02-22 00:40:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Downloaded 5.8 Kb in 0.072231s from omnipathdb.org (80.4 Kb/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.019834s, Pretransfer: 0.053402s, First byte at: 0.072215s
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1]
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:56] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:56] [TRACE]   [OmnipathR] Downloaded 3.8 Kb in 0.094944s from omnipathdb.org (39.7 Kb/s); Redirect: 0s, DNS look up: 0.000983s, Connection: 0.022812s, Pretransfer: 0.072633s, First byte at: 0.094851s
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1]
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:57] [SUCCESS] [OmnipathR] Downloaded 424 annotation records.
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Downloaded 36.9 Kb in 0.104972s from omnipathdb.org (351.5 Kb/s); Redirect: 0s, DNS look up: 0.001086s, Connection: 0.023616s, Pretransfer: 0.05667s, First byte at: 0.101827s
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:57] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:40:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.099769s from omnipathdb.org (87.4 Kb/s); Redirect: 0s, DNS look up: 0.001069s, Connection: 0.020857s, Pretransfer: 0.071991s, First byte at: 0.099601s
[2025-02-22 00:40:58] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:58] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-02-22 00:40:58] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:58] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-02-22 00:40:58] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-22 00:40:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-22 00:40:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-22 00:40:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:40:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:40:59] [TRACE]   [OmnipathR] Downloaded 4.7 Mb in 0.566927s from omnipathdb.org (8.4 Mb/s); Redirect: 0s, DNS look up: 0.00106s, Connection: 0.01774s, Pretransfer: 0.052173s, First byte at: 0.085472s
[2025-02-22 00:40:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-22 00:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:40:59] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:40:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-02-22 00:41:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-02-22 00:41:00] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2025-02-22 00:41:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:00] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:00] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2025-02-22 00:41:01] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-02-22 00:41:01] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:41:01] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2025-02-22 00:41:01] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 23:24:31 UTC; omnipath
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 23:25:38 UTC; unix
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-22 00:41:03] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-22 00:41:03] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Contains 20 files.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-22 00:41:03] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:03] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] HTTP 200
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Downloaded 31 Kb in 0.424075s from www.ensembl.org (73.1 Kb/s); Redirect: 0s, DNS look up: 0.001359s, Connection: 0.019946s, Pretransfer: 0.091431s, First byte at: 0.407393s
[2025-02-22 00:41:04] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:04] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:41:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:04] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:41:04] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.109628s from omabrowser.org (985.5 Kb/s); Redirect: 0s, DNS look up: 0.001037s, Connection: 0.011492s, Pretransfer: 0.044348s, First byte at: 0.057754s
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-22 00:41:04] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:04] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:04] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:04] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Downloaded 29.2 Kb in 0.10368s from omnipathdb.org (281.2 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.018149s, Pretransfer: 0.06613s, First byte at: 0.100509s
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:05] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Downloaded 157.2 Kb in 0.226951s from static-content.springer.com (692.7 Kb/s); Redirect: 0s, DNS look up: 0.008664s, Connection: 0.015282s, Pretransfer: 0.047731s, First byte at: 0.206682s
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:05] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:06] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.293703s from omnipathdb.org (7 Mb/s); Redirect: 0s, DNS look up: 0.00099s, Connection: 0.020572s, Pretransfer: 0.072011s, First byte at: 0.111044s
[2025-02-22 00:41:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-02-22 00:41:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:06] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-02-22 00:41:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-02-22 00:41:07] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-02-22 00:41:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:07] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:10] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-22 00:41:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-22 00:41:10] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-22 00:41:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:11] [TRACE]   [OmnipathR] Downloaded 2.4 Mb in 0.319795s from omnipathdb.org (7.5 Mb/s); Redirect: 0s, DNS look up: 0.000873s, Connection: 0.016707s, Pretransfer: 0.065489s, First byte at: 0.096921s
[2025-02-22 00:41:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-22 00:41:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:11] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:12] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Downloaded 110.8 Kb in 0.147649s from omnipathdb.org (750.1 Kb/s); Redirect: 0s, DNS look up: 0.000996s, Connection: 0.021068s, Pretransfer: 0.06613s, First byte at: 0.106137s
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:12] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:12] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Downloaded 310.9 Kb in 0.17586s from omnipathdb.org (1.7 Mb/s); Redirect: 0s, DNS look up: 0.000961s, Connection: 0.021817s, Pretransfer: 0.054656s, First byte at: 0.096736s
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:13] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Downloaded 251.9 Kb in 0.142566s from omnipathdb.org (1.7 Mb/s); Redirect: 0s, DNS look up: 0.000962s, Connection: 0.018309s, Pretransfer: 0.05112s, First byte at: 0.086259s
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:13] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:13] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:14] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Downloaded 157.9 Kb in 0.125586s from omnipathdb.org (1.2 Mb/s); Redirect: 0s, DNS look up: 0.000944s, Connection: 0.017991s, Pretransfer: 0.051117s, First byte at: 0.085558s
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:14] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:14] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-22 00:41:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:14] [TRACE]   [OmnipathR] Downloaded 306.2 Kb in 0.154521s from omnipathdb.org (1.9 Mb/s); Redirect: 0s, DNS look up: 0.000894s, Connection: 0.020259s, Pretransfer: 0.053409s, First byte at: 0.092631s
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:15] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-22 00:41:15] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Downloaded 1.5 Mb in 0.217085s from omnipathdb.org (6.9 Mb/s); Redirect: 0s, DNS look up: 0.001116s, Connection: 0.020162s, Pretransfer: 0.053379s, First byte at: 0.091686s
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:15] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-02-22 00:41:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-02-22 00:41:16] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-02-22 00:41:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:16] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:17] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Downloaded 13.1 Kb in 0.098567s from omnipathdb.org (132.9 Kb/s); Redirect: 0s, DNS look up: 0.001049s, Connection: 0.022014s, Pretransfer: 0.056061s, First byte at: 0.098288s
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:17] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:17] [TRACE]   [OmnipathR] Downloaded 12.1 Kb in 0.095239s from omnipathdb.org (127 Kb/s); Redirect: 0s, DNS look up: 0.000911s, Connection: 0.021138s, Pretransfer: 0.05436s, First byte at: 0.094978s
[2025-02-22 00:41:18] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:18] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-02-22 00:41:18] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:18] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:18] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Downloaded 11.7 Kb in 0.106822s from omnipathdb.org (109.6 Kb/s); Redirect: 0s, DNS look up: 0.000885s, Connection: 0.021269s, Pretransfer: 0.065754s, First byte at: 0.106597s
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:19] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Downloaded 1 Mb in 0.225195s from omnipathdb.org (4.7 Mb/s); Redirect: 0s, DNS look up: 0.000856s, Connection: 0.020069s, Pretransfer: 0.06863s, First byte at: 0.106777s
[2025-02-22 00:41:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:20] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-22 00:41:20] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:20] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:20] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Downloaded 20.2 Kb in 0.121342s from omnipathdb.org (166.1 Kb/s); Redirect: 0s, DNS look up: 0.000951s, Connection: 0.022766s, Pretransfer: 0.074522s, First byte at: 0.118469s
[2025-02-22 00:41:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:21] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-02-22 00:41:21] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-22 00:41:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:21] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-02-22 00:41:21] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-22 00:41:23] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-22 00:41:23] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:23] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-02-22 00:41:23] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-22 00:41:23] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’

SUMMARY: processing the following file failed:
  ‘cosmos.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 4 WARNINGs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-22_0007/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-02-22 00:41:32 CET ]